cutadapt: error:
*It appears you want to trim paired-end data because you provided two input files, but then you also need to provide two output files (with -o and -p) or use the --interleaved option.*

But I just want to take the adapters from the files I am not looking to do it in the same way I would do with a single file is there any way to do this because if I try to do --interleaved I get:

cutadapt: error: Character '/' in adapter sequence 'RTNS/NEW/ADAPTERS/ILLTNEXTERAPE.FA' is not a valid IUPAC code. Use only characters XACGTURYSWKMBDHVN.

$\begingroup$I see a number of issues with your code: 1. Why does the first loop have a \ after LotsOfRaws? 2. In your second loop, you're passing in the entire file path as $file, whereas you should be setting something like file_bn=$(basename $file) and using $file_bn instead of $file with the -o option.$\endgroup$
– Ram RSJul 12 '19 at 23:26

Your next attempt, with --interleaved failed because the -a option expects an actual sequence, not a file unless you use it with file:. See cutadapt --help (emphasis mine):

Finding adapters:
Parameters -a, -g, -b specify adapters to be
removed from each read (or from the first read in a pair if data is
paired). If specified multiple times, only the best matching adapter
is trimmed (but see the --times option). When the special notation
'file:FILE' is used, adapter sequences are read from the given FASTA
file.

So, the -a expects to be given a sequence unless you use it as -a file:/path/to/file. Because you used it as -a runs/new/Adapters/IlluNexteraPE.fa instead of -a file:withruns/new/Adapters/IlluNexteraPE.fa, it tried to interpret runs/new/Adapters/IlluNexteraPE.fa as a sequence and complained because the character / isn't valid in a DNA sequence.

Finally, your last lop failed because you're giving the wrong name. The first rule of debugging is "print all the things". When you see a command that doesn't work as you expect, your first step should always be to print out the command and see what is actually being run. When you do a for file in /long/path/to/file loop, the entire path is included in your $file variable. Try running this:

What you need is to take the name of the file, without the path. And you don't want to escape the slash after LotsofRaws. So putting all this together and going back to your first attempt, what you want is something like this: